Study Capture sequences as Probes Solid surface Virus subtypes detected/targets used Detection methods Li et al., 2001 Multiple fragments of the hemagglutinin, neuraminidase, and matrix protein genes converted into cDNA of average size of 500 bases were used as probes. Glass slides Influenza A H1N1, H3N2 and H2N2 viruses. Viral RNAs were reverse transcribed and amplified by PCR, and the products were labeled with cyanine dyes. GenePix (Axon Instruments) or ChipReader (Virtek) confocal scanners, and the fluorescence were quantitated using ImaGene software (Biodiscovery). Sengupta et al., 2003 A collection of 476 influenza virus-specific oligonucleotides was spotted onto glass slides as probes (21 nucleotide in length designed using VirOligo database). Glass slides H3N8, H3N2 and H1N1 influenza A viruses. Viral RNAs were reverse transcribed and amplified by PCR, and the products were labeled with cyanine dyes. Packard BioScience Scanarray 3000; Perkin-Elmer, Boston, Mass). Kesseler et al., 2006 (Flow-Thru-Chip) Twenty-nine oligonucleotide probes (45 to 65 bp) were designed for recognition of seven different genes: the matrix protein (MP) gene of influenza A virus (MP/A); the nonstructural (NS) gene of influenza B virus (NS/B); hemagglutinin genes H1, H3, H5; and neuraminidase genes N1 and N2. Highly conserved viral sequences were obtained from the National Center for Biotechnology Information (NCBI) database and segmented into two to seven overlapping pieces. The length of the overlapping domain between two consecutive gene segments was generally 10 to 15 bp, but exceptionally shorter (5 bp) or longer (25 bp) lengths were designed as a function of the sizes of the specific gene segments. silicon wafer Influenza A H1N1, H5N1, H3N2 and influenza B, B/Yamanashi/166/98 viruses. Viral RNAs were reverse transcribed and amplified by PCR using biotinylated primers, and the products were labeled with Horse radish peroxidase-streptavidin. MGX 2000 instrument and placed in the MGX 1200CL detection unit for chemiluminescence (CL) detection Townsend et al., 2006 (FluChip-55) 103 capture-label pairs based on HA, NA, M and NP gene sequences were used as probes. Glass slides Influenza A H1N1, H3N2, H5N1 and influenza B viruses. Influenza virus RNA was extracted, reverse transcribed with universal influenza A virus gene-specific primers (12) that contained a T7 promoter, amplified by PCR, transcribed back to RNA, and then fragmented. Labeled with a fluorophore. Bio-Rad Laboratories (Hercules, CA) VersArray scanner with detection at 532 nm, a laser power of 60, a photo multiplier tube sensitivity of 700 V, and a 5-μm resolution. Image contrast was optimized by using Photoshop (Adobe, San Jose, CA). Han et al., 2008 Fifty-two oligonucleotide probes (detective probe, DP) specific for all 25 subtype viruses were designed according to the gene sequences of the amplified target cDNAs and avian influenza A subtypes in the GenBank database using DNAstar, Bioedit, Primer 5.0, and OMIGA software. Glass slides Influenza A H1N1, H3N8, H4N6, H2N3, H5N2, H6N8, H7N1, H8N4, H9N2, H10N4, H11N9, H12N5, H13N6, H14N5 and H15N8 viruses. Viral RNAs were reverse transcribed and amplified by multiplex PCR using TAMRA-tagged primers. PerkinElmer Scan Array Gx plus scanner with detection at 532nm and laser power of 90. Gall et al., 2009 The array consists of one probe for the conserved matrix gene and 97 probes targeting the HA0 cleavage-site region. NanoChip 400 electronic microarray system Influenza A H1N1, H2N2, H2N3, H3N8, H4N6, H5N1, H5N2,, H5N9, H6N2, H6N5, H7N1, H7N3, H7N7, H9N2, H10N4, H10N8, H11N6, H12N5, H13N2, H13N8, H14N3, H15N6 and H16N3 viruses. Target RNA was reverse transcribed, amplified and biotin-labeled by a one-step pan haemagglutinin RT-PCR modified by use of biotinylated primers. NanoChip 400 system (Nanogen Inc.). Gall et al., 2009 99 Influenza A-specific oligonucleotide probes ArrayTube platform Influenza A H1N1, H2N2, H2N3, H3N2, H3N8. H4N6, H5N1, H5N2, H6N2, H6N5, H7N1 and  H7N7 viruses. Target RNA was reverse transcribed, amplified and biotin-labelled by a one-step pan haemagglutinin RT-PCR modified by use of biotinylated primers. In vitro-transcribed RNA from a synthetic gene was applied as a labeled positive control. ATR03 transmission reader (Clondiag) Huang et al.,2009 Eight targets: the matrix gene segment (M1) of influenza A virus; the nonstructural gene segment (NS) of influenza B virus; the HA genes H1, H3, and H5; and the NA genes N1 (H1), N2, and N1 (H5). Sequences were obtained from GenBank and the Influenza Sequence Database and were then aligned. Highly conserved regions were selected for primers and for capture and discriminator oligonucleotides. Electronic microarray Influenza A H1N1, H3N2, H5N1 and influenza B, B/Shanghai/361/ 2002 viruses. Five capture mixes, each containing 100 nM concentrations of two or three biotinylated capture oligonucleotides complementary to two different amplicons, were sequentially addressed for 15 s at 350 nA to a number of electrode sites equal to the number of samples being analyzed. Nanochip 400 (NC400) instrument (Nanogen, San Diego, CA). Kang et al., 2010 The oligonucleotide 59-mer probes were designed for Novel H1, N1 and M gene sequences, all other human seasonal influenza H1 and N1 sequences and swine H1 and N1 sequences were selected. Likewise, all human influenza virus isolates of subtypes H3N2 and H5N1 were selected. Glass slides Influenza A subtypes H1N1, H5N1, H7N7 and H9N2. Purified multiplex PCR product with incorporated aminoallyl-dUTP was further labeled with Cy3 or Cy5. ScanArray Gx PLUS (PerkinElmer). The fluorescence intensity was quantified by Genepix Pro5.0 software (PerkinElmer). Ryabinin et al.,2011 One 16X9 spot sub-array contained NA-specific probes, while another 16X24 spot sub-array contained HA-specific probes Glass slides Influenza A H5N1, H5N3, H1N1, H6N1, H7N1, H3N8, H10N7, H13N8 and H12N2. Cy- dyes were used to label the targets Slides were scanned using ScanArray Express 2.0 (Perkin Elmer) at 543 nm (Cy3) and 633 nm (Cy5). The images were analyzed with ScanArray Express software (Perkin Elmer). Tao et al., 2011(VereFlu) Clinically important influenza virus subtypes, including the 2009 pandemic influenza (H1N1) and H5N1 viruses. VereFlu chip H1N1,H3N2, H5N1 and influenza B viruses The entire instrument consisted of a computer, a thermal control system (TCS), which enables PCR thermal cycling, and a microarray optical reader (Lean s.r.l., Medolla, Italy).

Table 1: List of selective studies carried out on microarray platforms used for Influenza virus identification and subtyping.